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<link title="BarnesHut" rel="Chapter" href="BarnesHut.html"><title>Index of values</title>
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<body>
<center><h1>Index of values</h1></center>
<table>
<tr><td align="left"><br>B</td></tr>
<tr><td><a href="BarnesHut.html#VALbounds_of_bodies">bounds_of_bodies</a> [<a href="BarnesHut.html">BarnesHut</a>]</td>
<td><div class="info">
<code class="code">bounds_of_bodies bs</code> returns a bounds which completely enclose
	the given bodies <code class="code">bs</code>.
</div>
</td></tr>
<tr><td><a href="BarnesHut.html#VALbounds_size_squared">bounds_size_squared</a> [<a href="BarnesHut.html">BarnesHut</a>]</td>
<td><div class="info">
<code class="code">bounds_size_squared bds</code> returns the size squared of the given
	bounds (i.e.
</div>
</td></tr>
<tr><td align="left"><br>C</td></tr>
<tr><td><a href="BarnesHut.html#VALcenter">center</a> [<a href="BarnesHut.html">BarnesHut</a>]</td>
<td><div class="info">
<code class="code">center t</code> returns the center of mass of the tree <code class="code">t</code>
</div>
</td></tr>
<tr><td><a href="Genotypes.html#VALcheck_fields_nb">check_fields_nb</a> [<a href="Genotypes.html">Genotypes</a>]</td>
<td><div class="info">
<code class="code">check_fields_nb c</code>
</div>
</td></tr>
<tr><td><a href="BarnesHut.html#VALcontains">contains</a> [<a href="BarnesHut.html">BarnesHut</a>]</td>
<td><div class="info">
<code class="code">contains b t</code> returns <code class="code">true</code> if <code class="code">t</code> contains <code class="code">b</code>.
</div>
</td></tr>
<tr><td><a href="Tree.html#VALcreate">create</a> [<a href="Tree.html">Tree</a>]</td>
<td><div class="info">
<code class="code">create adj_mat dist_mat</code>
</div>
</td></tr>
<tr><td><a href="Dendogram.html#VALcreate">create</a> [<a href="Dendogram.html">Dendogram</a>]</td>
<td></td></tr>
<tr><td><a href="GenoMat.html#VALcreate">create</a> [<a href="GenoMat.html">GenoMat</a>]</td>
<td><div class="info">
<code class="code">create collec</code>
</div>
</td></tr>
<tr><td><a href="DistMat.html#VALcreate">create</a> [<a href="DistMat.html">DistMat</a>]</td>
<td></td></tr>
<tr><td><a href="GenoMat.html#VALcreateF">createF</a> [<a href="GenoMat.html">GenoMat</a>]</td>
<td><div class="info">
<code class="code">createF collec</code>
	*
</div>
</td></tr>
<tr><td><a href="GenoMat.html#VALcreateP">createP</a> [<a href="GenoMat.html">GenoMat</a>]</td>
<td><div class="info">
<code class="code">createP (genos, gsize)</code>
</div>
</td></tr>
<tr><td align="left"><br>D</td></tr>
<tr><td><a href="Genotype.html#VALdescription">description</a> [<a href="Genotype.html">Genotype</a>]</td>
<td><div class="info">
<code class="code">description g</code>
</div>
</td></tr>
<tr><td><a href="Genotype.html#VALdiff">diff</a> [<a href="Genotype.html">Genotype</a>]</td>
<td><div class="info">
<code class="code">diff g1 g2</code>
</div>
</td></tr>
<tr><td><a href="BarnesHut.html#VALdo_add_force_on">do_add_force_on</a> [<a href="BarnesHut.html">BarnesHut</a>]</td>
<td></td></tr>
<tr><td><a href="BarnesHut.html#VALdo_calc_force">do_calc_force</a> [<a href="BarnesHut.html">BarnesHut</a>]</td>
<td></td></tr>
<tr><td><a href="BarnesHut.html#VALdo_calc_forces">do_calc_forces</a> [<a href="BarnesHut.html">BarnesHut</a>]</td>
<td></td></tr>
<tr><td align="left"><br>E</td></tr>
<tr><td><a href="GenoMat.html#VALempty">empty</a> [<a href="GenoMat.html">GenoMat</a>]</td>
<td><div class="info">
<code class="code">empty dim</code>
</div>
</td></tr>
<tr><td><a href="GenoMat.html#VALemptyF">emptyF</a> [<a href="GenoMat.html">GenoMat</a>]</td>
<td><div class="info">
<code class="code">emptyF dim</code>
</div>
</td></tr>
<tr><td align="left"><br>F</td></tr>
<tr><td><a href="BarnesHut.html#VALfold">fold</a> [<a href="BarnesHut.html">BarnesHut</a>]</td>
<td><div class="info">
<code class="code">fold fn start t</code> is the fundamental tree iterator.
</div>
</td></tr>
<tr><td><a href="DistMat.html#VALfold_left">fold_left</a> [<a href="DistMat.html">DistMat</a>]</td>
<td></td></tr>
<tr><td><a href="DistMat.html#VALfold_right">fold_right</a> [<a href="DistMat.html">DistMat</a>]</td>
<td></td></tr>
<tr><td align="left"><br>G</td></tr>
<tr><td><a href="DynMat.html#VALget">get</a> [<a href="DynMat.html">DynMat</a>]</td>
<td></td></tr>
<tr><td><a href="GenoMat.html#VALget">get</a> [<a href="GenoMat.html">GenoMat</a>]</td>
<td><div class="info">
<code class="code">get matrix i j</code>
</div>
</td></tr>
<tr><td><a href="DistMat.html#VALget">get</a> [<a href="DistMat.html">DistMat</a>]</td>
<td></td></tr>
<tr><td><a href="GenoMat.html#VALgetF">getF</a> [<a href="GenoMat.html">GenoMat</a>]</td>
<td><div class="info">
<code class="code">getF matrix i j</code>
</div>
</td></tr>
<tr><td><a href="DynMat.html#VALget_diff">get_diff</a> [<a href="DynMat.html">DynMat</a>]</td>
<td></td></tr>
<tr><td><a href="Dendogram.html#VALget_homology">get_homology</a> [<a href="Dendogram.html">Dendogram</a>]</td>
<td><div class="info">
<code class="code">getHomology tree</code>
</div>
</td></tr>
<tr><td><a href="Dendogram.html#VALget_pos">get_pos</a> [<a href="Dendogram.html">Dendogram</a>]</td>
<td><div class="info">
<code class="code">getPos tree</code>
</div>
</td></tr>
<tr><td align="left"><br>H</td></tr>
<tr><td><a href="Dendogram.html#VALheader">header</a> [<a href="Dendogram.html">Dendogram</a>]</td>
<td><div class="info">
<code class="code">header width height</code>
</div>
</td></tr>
<tr><td><a href="Dendogram.html#VALheight">height</a> [<a href="Dendogram.html">Dendogram</a>]</td>
<td><div class="info">
<code class="code">height tree</code>
</div>
</td></tr>
<tr><td><a href="Dendogram.html#VALhomology">homology</a> [<a href="Dendogram.html">Dendogram</a>]</td>
<td><div class="info">
<code class="code">homology geno_size diff</code>
</div>
</td></tr>
<tr><td align="left"><br>I</td></tr>
<tr><td><a href="BarnesHut.html#VALin_bounds">in_bounds</a> [<a href="BarnesHut.html">BarnesHut</a>]</td>
<td><div class="info">
<code class="code">in_bounds bds v</code> checks whether <code class="code">v</code> is in the bounds given by
	<code class="code">bds</code>.
</div>
</td></tr>
<tr><td><a href="DistMat.html#VALinit">init</a> [<a href="DistMat.html">DistMat</a>]</td>
<td></td></tr>
<tr><td><a href="DistMat.html#VALiter">iter</a> [<a href="DistMat.html">DistMat</a>]</td>
<td></td></tr>
<tr><td><a href="DistMat.html#VALiterij">iterij</a> [<a href="DistMat.html">DistMat</a>]</td>
<td></td></tr>
<tr><td align="left"><br>L</td></tr>
<tr><td><a href="Tree.html#VALleaves_nb">leaves_nb</a> [<a href="Tree.html">Tree</a>]</td>
<td><div class="info">
<code class="code">leaves_nb t</code>
</div>
</td></tr>
<tr><td><a href="Dendogram.html#VALleaves_nb">leaves_nb</a> [<a href="Dendogram.html">Dendogram</a>]</td>
<td><div class="info">
<code class="code">leavesNb tree</code>
</div>
</td></tr>
<tr><td><a href="Clustering.html#VALleaves_of_tree">leaves_of_tree</a> [<a href="Clustering.html">Clustering</a>]</td>
<td><div class="info">
<code class="code">leavesOfTree tree</code>
</div>
</td></tr>
<tr><td align="left"><br>M</td></tr>
<tr><td><a href="BarnesHut.html#VALmake_null_bounds">make_null_bounds</a> [<a href="BarnesHut.html">BarnesHut</a>]</td>
<td><div class="info">
<code class="code">make_null_bounds ()</code> returns a fresh set of bounds which enclose
	<b>no</b> possible object.
</div>
</td></tr>
<tr><td><a href="DistMat.html#VALmap">map</a> [<a href="DistMat.html">DistMat</a>]</td>
<td></td></tr>
<tr><td><a href="DistMat.html#VALmapij">mapij</a> [<a href="DistMat.html">DistMat</a>]</td>
<td></td></tr>
<tr><td><a href="Genotype.html#VALmarkers_nb">markers_nb</a> [<a href="Genotype.html">Genotype</a>]</td>
<td><div class="info">
<code class="code">markers_nb gs</code>
</div>
</td></tr>
<tr><td><a href="BarnesHut.html#VALmass">mass</a> [<a href="BarnesHut.html">BarnesHut</a>]</td>
<td><div class="info">
<code class="code">mass t</code> returns the mass of the tree <code class="code">t</code>
</div>
</td></tr>
<tr><td><a href="BarnesHut.html#VALmass_barycenter">mass_barycenter</a> [<a href="BarnesHut.html">BarnesHut</a>]</td>
<td><div class="info">
<code class="code">mass_barycenter sts</code>
</div>
</td></tr>
<tr><td><a href="BarnesHut.html#VALmass_trees">mass_trees</a> [<a href="BarnesHut.html">BarnesHut</a>]</td>
<td><div class="info">
<code class="code">mass sts</code>
</div>
</td></tr>
<tr><td><a href="DistMat.html#VALmax">max</a> [<a href="DistMat.html">DistMat</a>]</td>
<td></td></tr>
<tr><td><a href="Dendogram.html#VALmin_homology">min_homology</a> [<a href="Dendogram.html">Dendogram</a>]</td>
<td><div class="info">
<code class="code">minHomology tree</code>
</div>
</td></tr>
<tr><td><a href="DistMat.html#VALmk_dist">mk_dist</a> [<a href="DistMat.html">DistMat</a>]</td>
<td></td></tr>
<tr><td><a href="Dendogram.html#VALmk_leaf">mk_leaf</a> [<a href="Dendogram.html">Dendogram</a>]</td>
<td><div class="info">
<code class="code">mkLeaf i</code>
</div>
</td></tr>
<tr><td><a href="Dendogram.html#VALmk_node">mk_node</a> [<a href="Dendogram.html">Dendogram</a>]</td>
<td><div class="info">
<code class="code">mkNode t1 t2 h</code>
</div>
</td></tr>
<tr><td><a href="DistMat.html#VALmodif">modif</a> [<a href="DistMat.html">DistMat</a>]</td>
<td></td></tr>
<tr><td><a href="DistMat.html#VALmodifij">modifij</a> [<a href="DistMat.html">DistMat</a>]</td>
<td></td></tr>
<tr><td align="left"><br>O</td></tr>
<tr><td><a href="DynMat.html#VALof_mat">of_mat</a> [<a href="DynMat.html">DynMat</a>]</td>
<td></td></tr>
<tr><td align="left"><br>P</td></tr>
<tr><td><a href="Tree.html#VALprim_complete">prim_complete</a> [<a href="Tree.html">Tree</a>]</td>
<td><div class="info">
Prim's algorithm finds a minimum spanning tree, here from a complete graph
	given a distance matrix
</div>
</td></tr>
<tr><td><a href="DynMat.html#VALprint">print</a> [<a href="DynMat.html">DynMat</a>]</td>
<td></td></tr>
<tr><td><a href="GenoMat.html#VALprint">print</a> [<a href="GenoMat.html">GenoMat</a>]</td>
<td></td></tr>
<tr><td><a href="GenoMat.html#VALprintF">printF</a> [<a href="GenoMat.html">GenoMat</a>]</td>
<td></td></tr>
<tr><td><a href="DynMat.html#VALprint_line">print_line</a> [<a href="DynMat.html">DynMat</a>]</td>
<td></td></tr>
<tr><td align="left"><br>R</td></tr>
<tr><td><a href="Genotypes.html#VALread_file">read_file</a> [<a href="Genotypes.html">Genotypes</a>]</td>
<td><div class="info">
<code class="code">read_file file_name</code> reads a file
</div>
</td></tr>
<tr><td><a href="Genotypes.html#VALread_line">read_line</a> [<a href="Genotypes.html">Genotypes</a>]</td>
<td><div class="info">
<code class="code">read_line s</code>
</div>
</td></tr>
<tr><td><a href="Genotypes.html#VALread_lines">read_lines</a> [<a href="Genotypes.html">Genotypes</a>]</td>
<td><div class="info">
<code class="code">read_lines lines</code> reads an enumeration of lines
</div>
</td></tr>
<tr><td><a href="Genotypes.html#VALread_markers">read_markers</a> [<a href="Genotypes.html">Genotypes</a>]</td>
<td><div class="info">
<code class="code">read_markers s</code>
</div>
</td></tr>
<tr><td><a href="DynMat.html#VALrem_col">rem_col</a> [<a href="DynMat.html">DynMat</a>]</td>
<td></td></tr>
<tr><td align="left"><br>S</td></tr>
<tr><td><a href="DistMat.html#VALset">set</a> [<a href="DistMat.html">DistMat</a>]</td>
<td></td></tr>
<tr><td><a href="Tree.html#VALsize">size</a> [<a href="Tree.html">Tree</a>]</td>
<td><div class="info">
<code class="code">size t</code>
</div>
</td></tr>
<tr><td><a href="Genotype.html#VALsize">size</a> [<a href="Genotype.html">Genotype</a>]</td>
<td><div class="info">
<code class="code">size g</code>
</div>
</td></tr>
<tr><td><a href="BarnesHut.html#VALsquare">square</a> [<a href="BarnesHut.html">BarnesHut</a>]</td>
<td></td></tr>
<tr><td><a href="BarnesHut.html#VALsub_bounds">sub_bounds</a> [<a href="BarnesHut.html">BarnesHut</a>]</td>
<td><div class="info">
<code class="code">sub_bounds bds</code> returns an array of the 2^d (where d is the
	dimension of the space---<code class="code">bs</code> is 2*d elements long) sub-bounds of
	the <code class="code">bds</code> obtained by splitting the bounds in half on each
	dimension.
</div>
</td></tr>
<tr><td align="left"><br>T</td></tr>
<tr><td><a href="GenoMat.html#VALtoFloat">toFloat</a> [<a href="GenoMat.html">GenoMat</a>]</td>
<td><div class="info">
<code class="code">toFloat m</code> maps <code class="code">float_of_int</code> on <code class="code">m</code>
</div>
</td></tr>
<tr><td><a href="BarnesHut.html#VALtree_of_bodies">tree_of_bodies</a> [<a href="BarnesHut.html">BarnesHut</a>]</td>
<td><div class="info">
<code class="code">tree_of_bodies bs</code>
</div>
</td></tr>
<tr><td><a href="BarnesHut.html#VALtree_of_bodies_array">tree_of_bodies_array</a> [<a href="BarnesHut.html">BarnesHut</a>]</td>
<td><div class="info">
<code class="code">tree_of_bodies_array bs</code>
</div>
</td></tr>
<tr><td align="left"><br>U</td></tr>
<tr><td><a href="DynMat.html#VALunsafe_get">unsafe_get</a> [<a href="DynMat.html">DynMat</a>]</td>
<td></td></tr>
<tr><td><a href="DistMat.html#VALunsafe_get">unsafe_get</a> [<a href="DistMat.html">DistMat</a>]</td>
<td></td></tr>
<tr><td><a href="Clustering.html#VALupgma">upgma</a> [<a href="Clustering.html">Clustering</a>]</td>
<td><div class="info">
<code class="code">upgma distance_matrix genotypes_collection</code>
</div>
</td></tr>
<tr><td align="left"><br>W</td></tr>
<tr><td><a href="Dendogram.html#VALwrite_svg">write_svg</a> [<a href="Dendogram.html">Dendogram</a>]</td>
<td><div class="info">
<code class="code">write_svg out ~links_info ddg</code>
   prints the tree as an svg picture in <code class="code">out</code>
</div>
</td></tr>
<tr><td><a href="Dendogram.html#VALwrite_svg_file">write_svg_file</a> [<a href="Dendogram.html">Dendogram</a>]</td>
<td><div class="info">
<code class="code">write_svg_file file ~links_info ddg</code>
   prints the tree as an svg picture in <code class="code">file</code> and closes it
</div>
</td></tr>
<tr><td><a href="Dendogram.html#VALwrite_svg_leaves">write_svg_leaves</a> [<a href="Dendogram.html">Dendogram</a>]</td>
<td></td></tr>
<tr><td><a href="Dendogram.html#VALwrite_svg_nodes">write_svg_nodes</a> [<a href="Dendogram.html">Dendogram</a>]</td>
<td></td></tr>
</table><br>
</body>
</html>